Susanne Hummel

DNA preservation: a microsatellite-DNA study on ancient skeletal remains.

To determine the effect of environmental factors on the preservation of DNA, archeological teeth of approximately similar age but greatly differing site milieu were examined for DNA content. The complex relational system of locational milieu of the samples was reduced to its essential and, at the same time, easily measurable factors. These are temperature, humidity, pH value, the geochemical properties of the soil, the amount of postmortal organic substances and the general degree of microbial infestation in the respective soil. The relative DNA content in the samples was established by determining the rate of successful polymerase chain reaction (PCR) amplifications. Differences in quantity and quality of the results are attributed to the respective prevailing environmental factor or to the respective storage conditions. Dryness, low temperature and absence of microorganisms favors the preservation of DNA. The bioapatite of bones and teeth, like the DNA, are preserved under neutral or slightly alkaline conditions. Brief storage at room temperature does not affect the amount of amplifiable DNA but does affect the reproducibility of the results. Long storage outside a lab freezer reduces the amount and the reproducibility of DNA amplifications in ancient specimens.

Y-chromosome-specific DNA amplified in ancient human bone

Here, we report on the enzyme-directed amplification of human Y-chromosome-specific sequences from ancient bone material. This method allows one to identify the sex of skeletal remains on the DNA level

Optimized DNA extraction to improve reproducibility of short tandem repeat genotyping with highly degraded DNA as target

The reproducibility of short tandem repeat (STR) genotyping of highly degraded DNA is often reduced due to artifacts generated during polymerase chain reaction (PCR) amplification. The frequency and amount of these artifacts are related to the quality and quantity of the DNA amplified. Consequently, the aim of this investigation was the optimization of DNA extraction to increase the reproducibility of STR genotyping of samples containing highly degraded DNA. Starting from a standard extraction protocol, systematic variation of individual parameters resulted in optimized protocols for three categories of ancient human bone material (different degrees of DNA degradation) and a consensus protocol for the extraction of a broad range of ancient DNA preservation states.

Trace element studies on experimentally cremated bone. I. Alteration of the chemical composition at high temperatures

Abstract Trace element analysis has become a promising approach to discovering ancient lifestyles and subsistence for archaeologists and physical anthropologists. In Central Europe, however, human bodily remains consist of cremations for a period of approximately 2000 years. Published data on the elemental composition of cremations are scarce and there is a lack of detailed consideration of the element profiles of high temperature artifacts in cremated bones. This paper presents the first results of an experimental approach aimed at the assessment of in vivo elemental composition from bones which have been incinerated prior to inhumation. We conclude that in the case of cremated material, the trace element spectrum available for palaeodietary reconstruction is limited due to volatilization and crystal modification at higher temperatures. For Sr/Ca ratios however, which are most widely used for palaeodietary reconstruction, it is shown that an estimation of in vivo ratios from incinerated specimens is possible by regression analysis. Additional research required for a more detailed interpretation of the data is outlined.

Pre-Columbian population dynamics in coastal southern Peru: A diachronic investigation of mtDNA patterns in the Palpa region by ancient DNA analysis.

Alternative models have been proposed to explain the formation and decline of the south Peruvian Nasca culture, ranging from migration or invasion to autochthonous development and ecological crisis. To reveal to what extent population dynamic processes accounted for cultural development in the Nasca mainland, or were influenced by them, we analyzed ancient mitochondrial DNA of 218 individuals, originating from chronologically successive archaeological sites in the Palpa region, the Paracas Peninsula, and the Andean highlands in southern Peru. The sampling strategy allowed a diachronic analysis in a time frame from approximately 800 BC to 800 AD. Mitochondrial coding region polymorphisms were successfully analyzed and replicated for 130 individuals and control region sequences (np 16021-16408) for 104 individuals to determine Native American mitochondrial DNA haplogroups and haplotypes. The results were compared with ancient and contemporary Peruvian populations to reveal genetic relations of the archaeological samples. Frequency data and statistics show clear proximity of the Nasca populations to the populations of the preceding Paracas culture from Palpa and the Peninsula, and suggest, along with archaeological data, that the Nasca culture developed autochthonously in the Rio Grande drainage. Furthermore, the influence of changes in socioeconomic complexity in the Palpa area on the genetic diversity of the local population could be observed. In all, a strong genetic affinity between pre-Columbian coastal populations from southern Peru could be determined, together with a significant differentiation from ancient highland and all present-day Peruvian reference populations, best shown in the differential distribution of mitochondrial haplogroups.

Amplification of Y-chromosomal STRs from ancient skeletal material

The adaptation to ancient DNA analysis of a Y-chromosomal STR (short tandem repeat) multiplex comprising the four STR systems DYS19, DYS390, and DYS389I/II shows the suitability of Y-chromosomal STR typing on ancient human remains. A new primer site for the system, DYS389I/II, resulting in products shortened by 94 bp, was chosen to serve the special needs of amplification of ancient DNA. For the first time, it was possible to amplify STR loci of the Y chromosome from historical and prehistorical bones of up to 3000 years old.

Comparison of DNA extraction and amplification from ancient human bone and mummified soft tissue

South american precolumbian male mummies were employed as source material for a comparative investigation of bone and soft tissues by DNA analysis. The suitability of the DNA extracts from both sources was tested and evaluated by their effectiveness as target DNA in PCR amplifications. The results suggest that skeletal material should be given preference over soft tissues for PCR analysis if the material is severely degraded. This seems to be independent of the specific anatomical origin of the samples.ZusammenfassungFür eine vergleichende Untersuchung von Knochen und Weichgewebe als Quellenmaterial für DNA-Analysen wurden südamerikanische, präkolumbische, männliche Mumien verwendet. Die Eignung der DNA-Extrakte beider Quellen wurde über ihre Effektivität als Ziel-DNA in PCR-Amplifikationen bewertet. Die Ergebnisse zeigen, daß bei Verwendung stark degradierten Materials Knochen den Weichgeweben für PCR-Analysen vorzuziehen sind. Dies scheint unabhängig von der spezifischen anatomischen Herkunft der Proben zu sein.

Reconstruction of a historical genealogy by means of STR analysis and Y-haplotyping of ancient DNA

Archaeological excavations in St Margarethas church at Reichersdorf, Germany, in 1993 led to the discovery of eight skeletons, so far assumed to be of the Earls of Königsfeld, who used the church as a family sepulchre over a period of seven generations from 1546 to 1749. DNA-based sex testing and analysis of autosomal short tandem repeat systems (STR) was carried out to confirm the assumption of kinship. Since five of the individuals were determined as males, analysis of Y-specific STRs seemed feasible. A comparison of Y-haplotypes revealed that one individual could not be linked to the Königsfeld patrilineage, an observation supported by autosomal STR evidence. Two individuals typed as females posed an identification problem, since supposedly only male members of the family were buried in St Margarethas. Nevertheless, these individuals could tentatively be identified as members of the House of Königsfeld through genetic fingerprinting.

Diachronic Investigations of Mitochondrial and Y‐Chromosomal Genetic Markers in Pre‐Columbian Andean Highlanders from South Peru

This study examines the reciprocal effects of cultural evolution, and population dynamics in pre‐Columbian southern Peru by the analysis of DNA from pre‐Columbian populations that lived in the fringe area between the Andean highlands and the Pacific coast. The main objective is to reveal whether the transition from the Middle Horizon (MH: 650–1000 AD) to the Late Intermediate Period (LIP: 1000–1400 AD) was accompanied or influenced by population dynamic processes. Tooth samples from 90 individuals from several archaeological sites, dating to the MH and LIP, in the research area were collected to analyse mitochodrial, and Y‐chromosomal genetic markers. Coding region polymorphisms were successfully analysed and replicated for 72 individuals, as were control region sequences for 65 individuals and Y‐chromosomal single nucleotide polymorphisms (SNPs) for 19 individuals, and these were compared to a large set of ancient and modern indigenous South American populations. The diachronic comparison of the upper valley samples from both time periods reveals no genetic discontinuities accompanying the cultural dynamic processes. A high genetic affinity for other ancient and modern highland populations can be observed, suggesting genetic continuity in the Andean highlands at the latest from the MH. A significant matrilineal differentiation to ancient Peruvian coastal populations can be observed suggesting a differential population history.

Ancient DNA profiling by megaplex amplications

Simultaneous amplification of nine human short tandem repeat (STR) DNA sequences and the amelogenin locus allows reducing to an absolute minimum the amount of sample material that is necessary for genetic identification or kinship analysis. Valuable remains can be studied this way without any visible damage, as is demonstrated by typing the DNA of a tooth root from the Saxon warrior Widukind, who died about 1200 years ago. The broad applicability of the megaplex approach is shown by typing bone and teeth specimens ranging from a few months to 3000 years of age employing AmpFlSTR Profiler Plus. Additionally, megaplex STR typing is the method of choice for proving the authenticity of molecular results derived from ancient degraded DNA.